Vibrio vulnificus is a Gram-negative bacterium and an opportunistic pathogen that can cause septicemia or necrotizing fasciitis. Here, we report the draft genome sequences of 42 environmental V. vulnificus strains collected from the northern Gulf of Mexico. These data will allow for more robust comparisons between clinical and environmental strains.
ABSTRACT
Vibrio vulnificus is a Gram-negative bacterium and an opportunistic pathogen that can cause septicemia or necrotizing fasciitis. Here, we report the draft genome sequences of 42 environmental V. vulnificus strains collected from the northern Gulf of Mexico. These data will allow for more robust comparisons between clinical and environmental strains.
ANNOUNCEMENT
Vibrio vulnificus is a Gram-negative marine bacterium with a single polar flagellum (1). This bacterium is capable of producing necrotizing fasciitis if it enters the human body through broken skin or may cause sepsis if ingested, usually through the consumption of raw oysters (2). Previous studies have identified clinical and environmental ecotypes based on sequence polymorphism of the 16S rRNA gene (3) and the virulence-correlated gene (vcg) (4). Whole-genome sequencing has confirmed the existence of distinct clinical and environmental ecotypes (5), and the comparative analysis of clinical and environmental genomes has aided in the identification of genes likely required for virulence (6, 7). However, virulence remains poorly understood, and the lack of a large public collection of nonpathogenic genomes has been cited as a limitation (8). To address this data gap, we report the draft genome sequences of 42 environmental strains isolated from the northern Gulf of Mexico (NGOM).
The 42 environmental V. vulnificus strains were isolated previously from seven locations in the Texas segment of the NGOM between August 2006 and July 2007 (9). Isolates were cultured at 37°C overnight on tryptic soy blood agar (Remel, San Diego, CA) and confirmed as V. vulnificus with matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry (MALDI Biotyper; Bruker, Billerica, MA), as described previously (10). Genomic DNA was extracted with a QIAamp DNA minikit (Qiagen, Hilden, Germany) and quantified with a Qubit double-stranded DNA (dsDNA) broad-range (BR) assay kit (Fisher Scientific, Hampton, NH). Multiplexed paired-end libraries were prepared using a Nextera XT index kit (Illumina, San Diego, CA), per the manufacturer’s instructions, with the modification that libraries were normalized by the estimated genome size prior to pooling. Sequencing was completed using the Illumina MiSeq 500-cycle kit (v2) following standard FastQ-only generation protocols to produce 250-bp paired-end reads. Overlapping paired reads were merged with FLASH version 1.2.11 (option -M 300) (11). Adapter sequences and low-quality bases were trimmed using Trim Galore! version 0.4.0 (options -paired -retain_unpaired) (12). Trimmed reads for the 42 genomes were assembled using SPAdes version 3.9.0 (option -k 127) (13). The 42 genomes were also assembled using MaSuRCA version 3.2.8 (default options) (14) using the insert size distribution estimated with BWA (default options) (15). For this purpose, paired reads were aligned to a draft genome (assembled with SPAdes), and the mean insert size and standard deviation were estimated by parsing the final alignment (in SAM format) with an awk script (16). The draft genome assemblies were filtered by length (500-bp cutoff), and assembly metrics (e.g., total genome size [bp], number of contigs, N50 value, and G+C content [%]) were calculated by QUAST version 4.1 (default options) (17) to determine which assembler (SPAdes or MaSuRCA) produced a higher-quality genome. For the genomes of two strains, 18057 and 18063, MaSuRCA produced higher-quality assemblies. Draft genomes were annotated using the National Center for Biotechnology Information’s (NCBI’s) Prokaryotic Genome Annotation Pipeline (PGAP) (18).
Table 1 shows the assembly metrics for the 42 V. vulnificus genomes, including the overall genome size (bp), number of contigs, N50 value, and G+C content (%). The availability of these genomes will augment future comparative genomic analyses focused on the differentiation of clinical and environmental strains. Additionally, the availability of these genomes will advance the understanding of the environmental V. vulnificus reservoir.
TABLE 1.
Summary of the 42 Vibrio vulnificus draft genome assemblies from the northern Gulf of Mexico
| Isolate | GenBank accession no. | Genome size (bp) | No. of contigs | N50 value (bp) | G+C content (%) | Sequence coverage (×) | No. of coding genes | Provenancea |
|---|---|---|---|---|---|---|---|---|
| 18022 | RCGD00000000 | 4,845,321 | 65 | 270,380 | 46.75 | 123.8 | 4,544 | Aransas Bay, 2007 |
| 18023 | RCGC00000000 | 4,984,587 | 83 | 256,006 | 46.62 | 97.1 | 4,664 | Bird Island, 2007 |
| 18024 | RCGB00000000 | 4,941,116 | 111 | 117,910 | 46.68 | 96.34 | 4,540 | Bayside, 2007 |
| 18025 | RCGA00000000 | 5,240,241 | 176 | 90,860 | 46.47 | 82.96 | 4,999 | Bayside, 2007 |
| 18026 | RCFZ00000000 | 4,844,420 | 80 | 233,461 | 46.64 | 75.32 | 4,564 | Bayside, 2007 |
| 18027 | RCFY00000000 | 4,843,483 | 84 | 195,670 | 46.70 | 68.94 | 4,590 | Bayside, 2007 |
| 18028 | RCFX00000000 | 4,966,197 | 79 | 704,086 | 46.66 | 63 | 4,686 | Bayside, 2007 |
| 18029 | RCFW00000000 | 4,793,233 | 95 | 136,022 | 46.64 | 58.78 | 4,566 | Bayside, 2007 |
| 18030 | RCFV00000000 | 4,979,258 | 119 | 141,772 | 46.63 | 40.66 | 4,653 | Bayside, 2007 |
| 18031 | RCFU00000000 | 4,850,485 | 92 | 130,871 | 46.70 | 95.98 | 4,593 | Bayside, 2007 |
| 18032 | RCFT00000000 | 4,801,036 | 113 | 141,861 | 46.70 | 107 | 4,496 | Bayside, 2007 |
| 18033 | RBZB00000000 | 5,055,915 | 162 | 80,566 | 46.69 | 53.08 | 4,849 | Bayside, 2006 |
| 18034 | RBZD00000000 | 4,823,242 | 63 | 344,960 | 46.68 | 102.24 | 4,471 | Bayside, 2006 |
| 18035 | RBZH00000000 | 5,240,024 | 158 | 94,332 | 46.49 | 51.7 | 4,953 | Bayside, 2006 |
| 18036 | RBZG00000000 | 4,873,384 | 71 | 185,180 | 46.69 | 135.3 | 4,526 | Bayside, 2006 |
| 18037 | RBZF00000000 | 5,094,022 | 170 | 74,007 | 46.43 | 119.22 | 4,720 | Copano Bay, 2007 |
| 18038 | RBZE00000000 | 5,195,336 | 252 | 59,128 | 46.40 | 112.54 | 4,850 | Copano Bay, 2007 |
| 18039 | RBZJ00000000 | 4,988,278 | 99 | 208,583 | 46.61 | 58.08 | 4,678 | Copano Bay, 2007 |
| 18040 | RBZK00000000 | 4,840,145 | 79 | 145,069 | 46.69 | 139.02 | 4,450 | Copano Bay, 2007 |
| 18041 | RBZL00000000 | 5,412,903 | 82 | 235,674 | 46.51 | 86.9 | 5,035 | Copano Bay, 2007 |
| 18042 | RBZC00000000 | 4,933,479 | 57 | 393,935 | 46.82 | 104.6 | 4,492 | Copano Bay, 2007 |
| 18043 | RBZI00000000 | 4,905,570 | 90 | 202,561 | 46.66 | 60.38 | 4,614 | Copano Bay, 2007 |
| 18044 | RPGM00000000 | 4,935,504 | 82 | 207,050 | 46.63 | 59.44 | 4,706 | Copano Bay, 2007 |
| 18045 | RHHD00000000 | 4,800,809 | 82 | 147,435 | 46.77 | 42.42 | 4,469 | Copano Bay, 2007 |
| 18047 | RHHE00000000 | 4,820,655 | 103 | 125,851 | 46.78 | 41.88 | 4,429 | Copano Bay, 2007 |
| 18048 | RHHF00000000 | 5,082,584 | 94 | 209,253 | 46.72 | 144.84 | 4,816 | Copano Bay, 2007 |
| 18049 | RHHG00000000 | 4,907,792 | 104 | 224,385 | 46.66 | 99.46 | 4,612 | Copano Bay, 2007 |
| 18050 | RHHH00000000 | 4,957,444 | 99 | 210,035 | 46.69 | 89.38 | 4,663 | Copano Bay, 2007 |
| 18051 | RHHI00000000 | 4,927,428 | 75 | 187,128 | 46.79 | 52.24 | 4,496 | Copano Bay, 2007 |
| 18052 | RHHJ00000000 | 5,130,949 | 88 | 202,763 | 46.70 | 121.64 | 4,867 | Copano Bay, 2007 |
| 18053 | RPGN00000000 | 4,884,811 | 73 | 204,930 | 46.88 | 47.54 | 4,479 | Copano Bay, 2007 |
| 18054 | RHHK00000000 | 4,778,453 | 93 | 166,931 | 46.72 | 68.9 | 4,489 | Copano Bay, 2006 |
| 18055 | RHHL00000000 | 4,842,045 | 79 | 198,581 | 46.69 | 127.62 | 4,519 | Copano Bay, 2006 |
| 18056 | RBWJ00000000 | 4,929,131 | 44 | 304,520 | 46.86 | 105.94 | 4,490 | Copano Bay, 2007 |
| 18057 | RBWK00000000 | 4,931,307 | 79 | 213,852 | 46.71 | 132.62 | 4,699 | Cole Park, 2007 |
| 18058 | RBWL00000000 | 4,911,551 | 97 | 158,422 | 46.64 | 72.88 | 4,576 | Cole Park, 2006 |
| 18059 | RBWM00000000 | 4,799,654 | 65 | 294,393 | 46.76 | 144.34 | 4,479 | Cole Park, 2006 |
| 18060 | RBWN00000000 | 4,990,343 | 46 | 375,098 | 46.75 | 98.92 | 4,617 | Nueces Bay, 2007 |
| 18061 | RBWO00000000 | 5,081,056 | 36 | 450,849 | 46.56 | 119.28 | 4,721 | Nueces Bay, 2007 |
| 18062 | RBWP00000000 | 4,923,184 | 51 | 390,616 | 46.83 | 124.3 | 4,484 | Nueces Bay, 2007 |
| 18063 | RBWQ00000000 | 4,929,780 | 77 | 188,289 | 46.71 | 166.44 | 4,680 | Redfish Bay, 2007 |
| 18064 | RBWR00000000 | 5,057,894 | 117 | 130,275 | 46.70 | 90.8 | 4,816 | Redfish Bay, 2006 |
Provenance provided as location and year of collection. All locations are bodies of water in Texas.
Data availability.
These whole-genome shotgun projects have been deposited at GenBank under the accession numbers listed in Table 1. The raw sequence reads were deposited in the Sequence Read Archive under BioProject accession number PRJNA475262.
ACKNOWLEDGMENTS
We thank the Virginia Division of Consolidated Laboratory Services for providing MALDI-TOF testing and Illumina sequencing of the isolate collection. We also thank Lee J. Pinnell for his assistance with genome assembly.
Food and Drug Administration Cooperative Agreement funding for the Maintenance and Enhancement of ISO/IEC 17025 Accreditation and Whole Genome Sequencing for State Food Testing Laboratories supported the sequencing of this sample collection (grant 5U18FD006188-02). This cooperative agreement aims to build and diversify public pathogen genome databases.
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Associated Data
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Data Availability Statement
These whole-genome shotgun projects have been deposited at GenBank under the accession numbers listed in Table 1. The raw sequence reads were deposited in the Sequence Read Archive under BioProject accession number PRJNA475262.